Germline DNA methylation in six species of reef corals: patterns and potential roles in response to environmental change
DNA methylation is an epigenetic mark that plays an inadequately understood role in gene regulation, particularly in non-model species. Because it can be influenced by the environment and potentially transferred to subsequent generations, DNA methylation may contribute to the ability of organisms to acclimatize and adapt to environmental change. We evaluated the distribution of gene body methylation in reef-building corals, a group of organisms facing significant environmental challenges. Gene body methylation in six species of corals was inferred from in silico transcriptome analysis of CpG O/E, an estimate of germline DNA methylation that is highly correlated with patterns of methylation enrichment. Consistent with what has been documented in most other invertebrates, all corals exhibited bimodal distributions of germline methylation suggestive of distinct fractions of genes with high and low levels of methylation. The hypermethylated fractions were enriched with genes with housekeeping functions, while genes with inducible functions were highly represented in the hypomethylated fractions. In three of the coral species, we found that genes differentially expressed in response to thermal stress and ocean acidification exhibited significantly lower levels of methylation. These results support a link between gene body hypomethylation and transcriptional plasticity that may point to a role of DNA methylation in the response of corals to environmental change.
Temperature influence on DNA methylation in oysters
INTRODUCTION - DNA Methylation - Function in bivalves - MERV - Relationship with expression
The Variable Infiltration Capacity (VIC) Model, Version 5.0 - Improvements and New Applications.
Authors: Joseph Hamman1, Bart Nijssen1
Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
H070: Modeling Hydrological Processes and Changes
Abstract to be submitted to the American Geophysical Uninion 2015 Fall Meeting
Evaluation of Simulated Active Layer Depths in the Regional Arctic System Model
AUTHORS: Joseph Hamman¹, Bart Nijssen¹ 1. Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA. SESSION C017: Frozen soil, its change, and the responses and feedbacks of the frozen soil change in atmosphere, hydrology and ecosystem or GC046: Land Surface, Snow and Soil moisture in Land-climate Feedback and Model Diagnosis _Abstract to be submitted to the American Geophysical Uninion 2015 Fall Meeting_
Improving the land-surface components of Climate Forecast System Reanalysis (CFSR)
YEAR 2 PROGRESS REPORT NOAA Award: NA13OAR4310107 University of Washington PI: Bart Nijssen Reporting Period: 07/01/2014 - 06/30/2015 Report date: 06/30/2015
Sequence Data that never made it
INTRODUCTION Over the past several years our lab has experimented with a variety of high-throughput sequencing platforms with the ultimate goal of addressing important scientific questions. On a few occasions we have been successful. Some of our early work included Roche 454 GS-FLX pyrosequencing used to examine phenotypic plasticity in lake trout , identify single nucleotide polymorphisms in salmon and develop genomic resources for Pacific herring . - Morera D, Roher N, Ribas L, Balasch JC, Doñate C, Callol A, Boltaña A, Roberts SB, Goetz G, Goetz FW, Mackenzie SA. (2011) RNA-Seq reveals an integrated immune response in nucleated erythrocytes. PLoS ONE 6(10): e26998. doi:10.1371/journal.pone.0026998 - Gavery MR* and Roberts SB. (2012) Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 7:2 94-99 June 2012. doi:10.1016/j.cbd.2011.12.003 - Burge CA, Douglas N, Conti-Jerpe I, Weil E, Roberts SB, Friedman CS, CD Harvell. (2012) Friend or foe: the association of Labyrinthulomycetes with the Caribbean sea fan, Gorgonia ventalina. Diseases of Aquatic Organisms. 101:1-12 doi:10.3354/dao02487 - Gavery MR, Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc. PeerJ 1:e215 doi:10.7717/peerj.215 However there are a number of efforts that have failed early on (_ie_ poor read quality) or just never gained enough momentum to see the light of the peer-review system. This paper is a final attempt to share these datasets in a manner where they have the potenial, however slim, to be useful to someone. We will not be providing fluffy background or in-depth over-analysis but strive to offer a sound _data description_. This current work will be organized by target species, which will often correspond to project. Species include - _Vibrio tubiashii_ - Olympia oyster (_Ostrea lurida_) - Yellow Perch (_Perca flavescens_) - Pacific herring (_Clupea pallasii_) - Abalone / Withering Syndrome (WS) - Hard clam (_Mercenaria mercenaria_)